NM_000744.7:c.345C>T
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_000744.7(CHRNA4):c.345C>T(p.Ser115Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000059 in 1,611,404 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. S115S) has been classified as Uncertain significance.
Frequency
Consequence
NM_000744.7 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CHRNA4 | NM_000744.7 | c.345C>T | p.Ser115Ser | synonymous_variant | Exon 4 of 6 | ENST00000370263.9 | NP_000735.1 | |
CHRNA4 | NM_001256573.2 | c.-202C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 4 of 6 | NP_001243502.1 | |||
CHRNA4 | NM_001256573.2 | c.-202C>T | 5_prime_UTR_variant | Exon 4 of 6 | NP_001243502.1 | |||
CHRNA4 | NR_046317.2 | n.554C>T | non_coding_transcript_exon_variant | Exon 4 of 6 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000464 AC: 7AN: 150700Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.000100 AC: 25AN: 249814Hom.: 0 AF XY: 0.0000885 AC XY: 12AN XY: 135602
GnomAD4 exome AF: 0.0000602 AC: 88AN: 1460586Hom.: 1 Cov.: 32 AF XY: 0.0000688 AC XY: 50AN XY: 726602
GnomAD4 genome AF: 0.0000464 AC: 7AN: 150818Hom.: 0 Cov.: 30 AF XY: 0.0000272 AC XY: 2AN XY: 73638
ClinVar
Submissions by phenotype
Autosomal dominant nocturnal frontal lobe epilepsy Benign:1
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Inborn genetic diseases Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at